14 papers · ranked by Valyu relevance
Yangyang Li, Rendong Yang
Background With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a sequence alignment tool, faces limitations in performance efficiency and integration with modern…
Martin Larralde, Georg Zeller, Can Alkan
Protein similarity search and annotation is a key part of biological sequence analysis, allowing for the discovery of protein function from sequence data. Improving on Position-Specific Scoring Matrices that were used historically to search for motifs, Profile Hidden Markov Models (pHMMs) were introduced in HMMER () to…
M. Eric Irrgang, Caroline Davis, Peter M. Kasson, Dina Schneidman-Duhovny
'Dina Schneidman-Duhovny'] Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line…
Wanling Song, Robin A. Corey, T. Bertie Ansell, C. Keith Cassidy + 4 more
Interactions from Molecular Dynamics Simulations Authors: ['Wanling Song' 'Robin A. Corey' 'T. Bertie Ansell' 'C. Keith Cassidy' 'Michael R. Horrell' 'Anna L. Duncan' 'Phillip J. Stansfeld' 'Mark S. P. Sansom'] Lipids play important modulatory and structural roles for membrane proteins. Molecular dynamics simulations…
João Victor da Silva Guerra, Helder Veras Ribeiro-Filho, Gabriel Ernesto Jara, Leandro Oliveira Bortot + 2 more
Background Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the increasing availability of biostructural data due to advances in structural determination and…
Maria Littmann, Michael Heinzinger, Christian Dallago, Konstantin Weissenow + 1 more
'Konstantin Weissenow' 'Burkhard Rost'] One important aspect of protein function is the binding of proteins to ligands, including small molecules, metal ions, and macromolecules such as DNA or RNA. Despite decades of experimental progress many binding sites remain obscure. Here, we proposed bindEmbed21, a method…
Žan Hafner Petrovski, Barbara Hribar-Lee, Zoran Bosnić, Kyriakos Kachrimanis
'Kyriakos Kachrimanis'] Identifying binding sites on the protein surface is an important part of computer-assisted drug design processes. Reliable prediction of binding sites not only assists with docking algorithms, but it can also explain the possible side-effects of a potential drug as well as its efficiency. In…
Uthpala Chandrasekara, Emilie M. Broussard, Darin R. Rokyta, Bryan G. Fry
'Bryan G. Fry'] The evolutionary interplay between predator and prey has significantly shaped the development of snake venom, a critical adaptation for subduing prey. This arms race has spurred the diversification of the components of venom and the corresponding emergence of resistance mechanisms in the prey and…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…
Vladislav Skorpil, Vaclav Oujezsky, Arcangelo Castiglione, Gianni D’Angelo
'Gianni D’Angelo'] This paper presents an implementation of the parallelization of genetic algorithms. Three models of parallelized genetic algorithms are presented, namely the Master-Slave genetic algorithm, the Coarse-Grained genetic algorithm, and the Fine-Grained genetic algorithm. Furthermore, these models are…
Shiqing Zhao, Yanhao Zhu, Ruizhou Li, Zeyu Xu + 7 more
Nanobody-antigen molecular recognition underpins nanobody discovery and development, necessitating accurate determination of binding occurrence, interface residues, and affinity. Current predictors are architecturally designed for the massive, heterogeneous spectrum of general protein-protein interactions, diluting the…
Izabella Lederer, Basmah Shahid, Uyen Dao, Alex Brogdon + 16 more
'Hannah Byrtus' 'Marcelin Delva' 'Orson Deva' 'Paige Hatfield' 'Mikayla Hertz' 'Jenna Justice' 'Sarah Mavor' 'Erin Pilbeam' 'Zoe Rice' 'Abbey Simpson' 'Hallie Temar' 'Richard Wynn' 'Joana Xhangolli' 'Chiron Graves' 'Hannah Seidel' 'Bruce Schnapp Dr.'] Melanophilin is a myosin adaptor required for transporting the…
Nezar Abdennur, Geoffrey Fudenberg, Ilya M Flyamer, Aleksandra A Galitsyna + 4 more
Operations on genomic intervals, also known as genomic ranges, are fundamental to bioinformatic analyses. These operations can be used to answer questions that include: Where is the closest enhancer to a gene of interest? How do chromatin states change across cell types? Which repeat elements contain binding sites for…
Tianze Cao, Qian Li, Yuexia Huang, Anshui Li
Background The visual sequence logo has been a hot area in the development of bioinformatics tools. ggseqlogo written in R language has been the most popular API since it was published. With the popularity of artificial intelligence and deep learning, Python is currently the most popular programming language. The…